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Nucleotide-free cryo-EM structure of E.COLI LPTB2FG transporter

Analyse Nucleotide-free cryo-EM structure of E.COLI LPTB2FG transporter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MHU
Type: protein
Length: 1,112 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipopolysaccharide export system permease protein lptf; Lipopolysaccharide export system…
EC: 3.6.3.-
UniProt: P0AF98, P0ADC6, P0A9V1
Ligands: JSG
Pockets: 18 · best druggability 0.84

Structure

electron microscopy · 3 distinct chains · 47% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	Lipopolysaccharide export system permease protein lptf	protein	311	50% helix, 2% strand	P0AF98
G	Lipopolysaccharide export system permease protein lptg	protein	341	51% helix, 6% strand	P0ADC6
A, B	Lipopolysaccharide export system ATP-binding protein lptb (EC 3.6.3.-)	protein	230	38% helix, 27% strand	P0A9V1

Ligands and binding sites

JSG · (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl) ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R}, 6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R}, 3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S}, 4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3, 4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R}) · ligand · chains F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1060	0.84	0.85	117	empty
2	492	0.76	0.84	46	empty
3	479	0.70	0.79	49	empty
4	154	0.68	0.88	36	empty
5	221	0.66	0.84	32	empty

Interfaces

4 interfaces between chains.

F–G · 1536 Å² buried · 4 hydrogen bonds · protein-protein
G–A · 957 Å² buried · 3 hydrogen bonds · protein-protein
F–B · 901 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 607 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6MHU · Nucleotide-free Cryo-EM Structure of E.coli LptB2FG Transporter · the same entry in another collection · chain F against F, TM-score 1.00
P0A9V1 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system ATP-binding… · a predicted model of the same protein · chain A against A, TM-score 0.94
P0ADC6 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system permease protein… · a predicted model of the same protein · chain G against A, TM-score 0.90
P0AF98 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system permease protein… · a predicted model of the same protein · chain F against A, TM-score 0.82

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0AF98
Every structure of UniProt P0ADC6
Every structure of UniProt P0A9V1
Elsewhere: RCSB PDB 6MHU · PDBe 6MHU · UniProt P0AF98 · UniProt P0ADC6 · UniProt P0A9V1

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